Oxford Protein Informatics Group

In this post I’ll walk through how to set up the CCDC Python API and use the CSD Geometry Analyser to evaluate the geometric quality of molecules from three representative structure-based de novo design models. I’ve put together a small GitHub repo with the full analysis code where we look at bond lengths, angles, torsions, and ring conformations across the three met...

Over the last few years, large language models (LLMs) have gone from being curiosities tucked away in research labs to something most of us interact with on a daily basis; whether for drafting emails, debugging code, or simply pondering the meaning of life at 2am. And yet, for all our reliance on these systems, a rather inconvenient truth lingers in the background: nobody, no...

When approaching the methods used in de-novo protein design, one is quickly confronted with a plethora of overlapping formulations of what looks superficially like “the same thing”. One paper trains an -prediction network with a simple MSE loss; another trains a score network with a stochastic-differential-equation justification; a third trains a clean-data predictor...

I got into protein modelling not long before AlphaFold2 first released. At that time some of the prevailing methods for protein structure prediction came from highly interpretable energy functionals that arose from a particularly beautiful intersection of statistical mechanics and biology. These “Potts” models are going to be the centre of a larger discussion in this blog on ...

The LLM boom is causing a global shortage of the very same computer memory it needs to sustain itself. Reports suggest OpenAI’s Stargate project alone could consume up to